Computer
Static scheduling algorithms for allocating directed task graphs to multiprocessors
ACM Computing Surveys (CSUR)
Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Massively Parallel Solutions for Molecular Sequence Analysis
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Banyan networks for partitioning multiprocessor systems
ISCA '73 Proceedings of the 1st annual symposium on Computer architecture
Parallel biological sequence comparison using prefix computations
Journal of Parallel and Distributed Computing
Faster genome annotation of non-coding RNA families without loss of accuracy
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Concurrency and Computation: Practice & Experience - Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004)
Programming languages and their compilers: Preliminary notes
Programming languages and their compilers: Preliminary notes
Techniques for hardware-accelerated parsing for network and bioinformatic applications
Techniques for hardware-accelerated parsing for network and bioinformatic applications
Sorting networks and their applications
AFIPS '68 (Spring) Proceedings of the April 30--May 2, 1968, spring joint computer conference
Fine-grained parallel RNA secondary structure prediction using SCFGs on FPGA
Parallel Computing
Accelerating ncRNA homology search with FPGAs
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
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The search for homologous RNA molecules---sequences of RNA that might behave simiarly due to similarity in their physical (secondary) structure---is currently a computationally intensive task. Moreover, RNA sequences are populating genome databases at a pace unmatched by gains in standard processor performance. While software tools such as Infernal can efficiently find homologies among RNA families and genome databases of modest size, the continuous advent of new RNA families and the explosive growth in volume of RNA sequences necessitate a faster approach. This work introduces two different architectures for accelerating the task of finding homologous RNA molecules in a genome database. The first architecture takes advantage of the tree-like configuration of the covariance models used to represent the consensus secondary structure of an RNA family and converts it directly into a highly-pipelined processing engine. Results for this architecture show a 24× speedup over Infernal when processing a small RNA model. It is estimated that the architecture could potentially offer several thousands of times speedup over Infernal on larger models, provided that there are sufficient hardware resources available. The second architecture is introduced to address the steep resource requirements of the first architecture. It utilizes a uniform array of processing elements and schedules all of the computations required to scan for an RNA homolog onto those processing elements. The estimated speedup for this architecture over the Infernal software package ranges from just under 20× to over 2,350×.